Ghosts in the Machines
by Del Rion
Summary: After everything that happened with the Mandarin and AIM, Tony attempts to regain a sense of normalcy in his life. It would seem, however, that he and the bots now share a common cause for anxiety: tremors. Part of the "Genius, AI & Bots" series. Written for Trope Bingo's round 2.
1. Part 1

**Story Info**

**Title:** Ghosts in the Machines

**Author:** Del Rion

**Fandom:** Iron Man (MCU)

**Era:** Takes place right before "The Fervid Defense Protocol"

**Genre:** Drama, hurt/comfort

**Rating:** T / FRT

**Characters:** J.A.R.V.I.S., Pepper Potts, Tony Stark (Iron Man), Tony's bots (DUM-E and U)

**Pairing:** Pepper/Tony

**Summary:** After everything that happened with the Mandarin and AIM, Tony attempts to regain a sense of normalcy in his life. It would seem, however, that he and the bots now share a common cause for anxiety: tremors.  
Complete. Part of the "Genius, AI & Bots" series.

**Written for:** My card on _Trope Bingo_'s Round 2 (square: "hurt/comfort")

**Warnings:** Poorly managed PTSD, a couple profanities. Contains Iron Man 3 spoilers.

**Disclaimer:** Iron Man, Avengers and Marvel Cinematic Universe, including characters and everything else, belong to Marvel, Marvel Studios, Jon Favreau, Joss Whedon, Shane Black, Paramount Pictures and Walt Disney Studios Motion Pictures. In short: I own nothing; this is pure fiction created to entertain likeminded fans for no profit whatsoever.

**Beta:** Mythra

**Feedback:** Always welcome ^^

* * *

**About ****_Ghosts in the Machines_****:** The events of _Iron Man 3_ are bound to leave their marks on Tony – as well as the bots.

This story quite directly sets up the events of "_The Fervid Defense Protocol_" (even featuring Mark 43 & 44!), although it isn't necessary to read one story to understand the other.

* * *

**Chapters and statuses:** Below you see the writing process of the story's chapters. If there is no text after the chapter's title, then it is finished and checked. Possible updates shall be marked after the title.

**Part 1**  
**Part 2**

* * *

. . .

* * *

**Part 1**

* * *

If nothing had been the same since New York – a name Tony still had some difficulty saying or hearing – then most certainly nothing had been the same since the Mandarin. Or, Aldrich Killian. Whatever.

There was also Extremis, and what the implications of Maya Hansen's life's work meant for Tony and Pepper. Mostly Pepper, but Tony had sorted that out to the best of his ability.

That wasn't to say that Extremis had changed nothing for Tony – far from it. Extremis enabled him to take the dreaded, nigh _impossible_ step to get the shrapnel removed from his chest – and with it, the arc reactor.

So, in summary, a lot of things had changed.

It felt like a pit-stop on the road to normalcy when Tony fixed up the bots; to see their familiar forms moving in his peripheral vision, or to hear their sounds of inquiry, joy or protestation.

Reconstructing the bots from the wreckage Tony had pulled from the bottom of the ocean was hard. He could have done a complete remodel, but Tony craved familiarity in the midst of all the changes, and the bots filled that role perfectly.

Tony's private fear – only ever spoken out loud in the presence of J.A.R.V.I.S. – was that the bots wouldn't be the same. He had back-ups of their operating systems and latest modifications, but a nagging doubt kept popping up in the back of his mind; that something might be missing or corrupted.

He wasn't entirely wrong to fear those things, even when the bots came back just as they had been.

The first lesson – and, frankly, the _only_ lesson Tony needed to learn in order to realize that not everything had gone back to normal with the bots –came when a magnitude 4.1 earthquake shook the Stark Industries housing complex where their temporary quarters were: Tony was jolted wide awake, confused, heart pounding madly.

_"Sir,"_ J.A.R.V.I.S. said in a quiet tone, perhaps to let Pepper sleep, _"are you planning on getting out of bed?"_

It was a strangely phrased question, as if J.A.R.V.I.S. were aiming at something the AI was yet to reveal.

"Probably," Tony whispered back. He wasn't gearing towards a panic attack, exactly, but he felt too uneasy to roll over and try to get back to sleep. So, he rolled off the bed, slipped into some clothes that lay close by, and left the bedroom as silently as possible; Pepper needed all the sleep she could get.

"What's up?" Tony asked as he headed for the stairs that led down to his temporary workshop. He didn't for a second think that J.A.R.V.I.S.'s earlier question was without ulterior motives.

_"The bots are uneasy, sir,"_ the AI replied. The sound system was crappy – just another thing Tony needed to fix – but this housing option was only temporary – or so Pepper kept telling him. Tony had a feeling she was biding her time before suggesting they move to New York City.

The mere idea sent shivers down his spine and a sensations of something hot and heavy being wedged between his inner organs.

Tony decided he wouldn't ask J.A.R.V.I.S. for a clarification on the bots; he was going down to the shop anyway, so, he would see for himself what 'uneasy' meant in bot language.

Once he arrived, Tony decided it meant the same as in English.

Dummy and You were huddled in a corner, letting out sounds of distress. Not previously unheard of sounds, either, because Mark 42 had picked them up just moments before Tony's Malibu house was washed into the ocean, and suddenly Tony didn't feel so great himself.

That's when another small aftershock shook the building.

Tony may have entertained the idea of telling the bots to stop being idiots, but the sounds the pair let out as tools rattled on the shelves tore at him.

There were no cracks on the floor or the walls; no sounds of explosions. Nevertheless, Tony once again had the _feeling_ that he'd experienced only seconds before gravity and falling mass pulled him to the bottom of the ocean.

In the corner, the bots whined pitifully.

Tony had scrubbed their memory banks to remove unnecessary data from the time of the attack on their home. Perhaps he should have had a heavier hand while doing it – or maybe this fear had corroded too deeply into the bots to be callously removed.

The building shivered again, just slightly; Tony would have missed it if he hadn't been attuned to every little vibration. You let out a shrill cry, and Tony was suddenly moving towards the bots without thinking; it was an instinct, to protect and to comfort; to seek safety in numbers.

Tony had never been a team player, but he had built the bots. They were his responsibility, and he had let them down when their home was torn to pieces.

The bots shifted minutely to accommodate Tony in their corner. As soon as he settled down between their newly reconstructed bodies, the bots moved in again, and Tony reached out for their hands, feeling mechanical parts squeeze his fingers. Up close, he could see You was actually trembling, and he had no idea why the bot was doing that, seeing as it had no physiological need for such a display of fear.

Of course, the answer was painfully simple: You was copying Tony's own responses from over the years. It broke his heart and he held onto the bot tighter – even though You could not tell the difference.

Dummy eventually let go of Tony's hand. Perhaps that was something copied from Tony, too; to fake bravado when he was actually ready to shit his pants. The bot didn't move away from their huddled group, though; Dummy simply moved his arm and settled the claws in Tony's hair, squeezing carefully, tugging on the strands. It didn't hurt, and the end result was weirdly comforting.

No more tremors took place – at least, not strong enough to be felt, even when Tony was waiting for them. The bots didn't move, and Tony wondered if this was how parents felt when their kids fell asleep after a nightmare.

_"Sir,"_ J.A.R.V.I.S. spoke up – so softly it was almost a whisper.

"Yeah?" Tony whispered back, as if not to wake the bots, which was ridiculous.

_"Miss Potts is awake and asking for your whereabouts. Shall I inform her?"_

Tony wavered. Pepper would guess he was in the shop, eventually, but it all came down to how J.A.R.V.I.S. would phrase his answer. "Tell her… Tell her that I'm in the shop but leave it at that."

_"Very well, sir."_

"J?"

_"Yes, sir?"_

"Let me know if she's headed this way." What was going on in the shop wasn't embarrassing, but it wasn't something Tony was proud of, either. Pepper worried enough as it was; she didn't need to see another ill reminder of what they had been through.

J.A.R.V.I.S. didn't reply, but Tony knew the AI could read between the lines. Just as J.A.R.V.I.S. had known Tony would come down to check on the bots, regardless of all the grief they gave him.

_to be continued…_


	2. Part 2

**Part 2**

* * *

It was one of the biggest quakes of the year.

Tony didn't care if it was the biggest of the century; he felt it, all the way in his gut, and he hated it.

Also, he was starting to have a problem with staying in California.

Pepper was in her office when the power went out, which was a precaution to prevent extensive damage should the tremors wreak any actual havoc. Tony, on the other hand, was in the workshop, working on Mark 44, when the lights went out. That never would have happened back in Malibu, with his extensive back-up generators.

So, Tony wasn't expecting the pitch black silence – especially when he was still getting used to the absence of light that came with the removal of the arc reactor.

The bots whined and moved frantically across the room, colliding with objects in the dark. The shaking continued for several more seconds and Tony found himself desperately clutching Mark 44's arm until it ended.

The darkness remained, only broken by self-powered machines – including two suits of armor.

"J," Tony called out carefully. When no response came, he felt his heart rate pick up painfully. His chest felt tighter, too, and it wasn't unlike the beginning phases of a panic attack he had learned to recognize by now.

_"Sir,"_ J.A.R.V.I.S.'s voice finally replied through Mark 43's speakers where the armor stood by the far wall. _"It would seem the power is down throughout the entire facility. If there are no further tremors, the power should be restored within half an hour."_

"Half an hour? Seriously?" Tony frowned.

_"The power restoration will happen in phases, to avoid placing too much stress on the generators. You personally designed that measure of precaution."_

"I must have been drunk," Tony muttered, but most likely he had been as sober as the day he was born.

He looked around, his eyes landing on the glowing circle on Mark 43's chest. Somewhere further off, the bots were huddled in the dark, tiny sounds of distress reaching Tony's ears.

It had to be his lizard brain that forced Tony through the darkness towards the bots. He couldn't find his way, though, and that put an unrealistic fear in his mind; they were in his temporary workshop, where he could hardly get lost.

"J, switch on the armor's external lights," Tony ordered, and the darkness was shoved back as Mark 43's various lights turned on. It created a wide area of well-lit room around the armor, exposing the bots in their corner as well, but Tony still got uneasy looking at the pitch-black edges that waited just outside the lit up area.

His lizard brain was still acting up, obviously, because Tony moved to the bots, grabbed a tarp from a shelf above them and shook it open, then looked at Mark 43. "J.A.R.V.I.S., can you access Mark 44?"

A moment of silence met his request. _"Yes, sir,"_ the AI finally replied and Mark 44 sat up on the table where Tony had been working on it.

"Bring them both over," Tony ordered and watched the two suits approach.

The darkness moved with Mark 43. Tony tried telling himself it was the lights, not the darkness, but he wasn't finding the optimistic thoughts he wanted.

_"Sir?"_ J.A.R.V.I.S. asked as the armors had reached him.

Tony offered the tarp to the suits. "Hold it up. You know, like a tent," he explained when Mark 44 grabbed onto the tarp and held it like a curtain. It took some navigating and arranging, but eventually Tony, the bots and two suits of armor were all under the tarp which was now draped around them, blocking out the rest of the room.

"Dim Mark 43's lights," Tony requested, squinting at the brightness. J.A.R.V.I.S. did as he was told, leaving the underside of the tarp in a pleasant lighting.

The bots looked around cautiously, then chirped happily, leaning their hands a bit closer to Tony's body.

"See? All better," Tony teased softly, patting their arms. "It's like camping – or hiding under a blanket in your bed during a thunderstorm."

_"The bots have never been camping, sir, and I do not think they are afraid of lightning."_

"Way to ruin this for everyone else, J," Tony complained.

_"My heartfelt apologies, sir. Shall I make nature sounds to further the illusion of camping?"_

"Now you're just being an ass on purpose." Tony debated telling the AI to leave, but that would take their only source of light. Of course, he could just tell J.A.R.V.I.S. to be silent, but that wasn't the same.

_"Are you feeling better, sir?"_ J.A.R.V.I.S. asked before Tony could make up his mind.

"Me?" Tony frowned.

_"Yes: the armor bio-scanners suggested distress at the time of the earthquake and the beginning of the power outage."_

"That is a normal human response," Tony claimed.

_"As is seeking refuge in numbers, in an easily defendable, enclosed location."_

Tony had a feeling J.A.R.V.I.S. wasn't buying into his camping excuse; the AI knew the tricks a human mind played on itself, inside and out. Plus, J.A.R.V.I.S. knew Tony better than most people ever would – inside and out.

"'Tis good," Tony murmured, because it was: under the tarp, with the two armors and the bots, any outside threat was rendered innocuous. It was an illusion, mostly, but Tony was too content within it to break the fourth wall just yet.

_"Very good, sir,"_ J.A.R.V.I.S. hummed, as if satisfied to accept this for the time being.

Time passed in the strange comfort of the tarp-tent. A few tremors came and went – aftershocks – and eventually Tony folded himself into a sitting position on the floor beside the bots, leaning against Mark 44's leg. J.A.R.V.I.S. had softened the lights to a soft glow, the arc reactors mounted on the armors' chests becoming the brightest lights once more.

Tony debated taking a nap.

He must have actually dozed off because he jerked painfully at Pepper's voice. "Tony?!"

Tony blinked, looking around. The bots were looking towards the sound of Pepper's voice; the two armors remained as they were, holding up the tarp.

"Tony… are you in there?" Pepper's voice had come closer, and then a hand cautiously pushed up the edge of the tarp.

The illusion of safety shattered around Tony, but it was soon replaced by mild shame.

"Hi," he greeted Pepper's perplexed expression.

"What are you –?"

"Camping," Tony said quickly. "The bots have never been camping, so…"

"You took them camping in your workshop, during a blackout?"

"Sure," Tony shrugged, as if it were no big deal or nothing to be amazed by.

Pepper's expression wavered for a bit. "Tony…" It was her '_I know you're not okay_' voice, and Tony had a deep dislike for it – mostly because he always put it there, and he wished he didn't.

"You should join us," Tony suggested.

"The power's back on in most of the factory and R&D areas," Pepper countered.

"So?" Tony asked, desperate to throw her off the scent of his momentary fear during the quake.

She took a tentative look at the armors and bots, as if considering what would be the lesser of many evils she was no doubt imagining.

"We'll make room," Tony promised, scooting over.

"I have a meeting that's already been delayed because of the power outage."

"Then why are you here?"

"To check on you; I was worried." Why exactly she had been worried when Tony was in the presence of two Iron Man armors, he didn't know. Perhaps she knew… After all, she read most of Tony's uneasiness like an open book these days. He didn't like that, but knew he had to let her close or she would take it the wrong way – like during all those times Tony had kept her at arm's length in the past.

"We're fine," Tony reassured her and patted Dummy to indicate he wasn't actually the only one with problems.

"Will you come out?" Pepper asked next.

"I was in the middle of fine-tuning Mark 44," Tony replied.

"Out from under the tarp, I meant," Pepper clarified.

"Oh." Tony considered it, knowing he couldn't huddle there forever. Finally he motioned at the armors, and J.A.R.V.I.S. interpreted the message and folded the tarp, leaving them exposed in their corner.

Pepper straightened carefully, her long legs towering over Tony. He looked up, giving her a soft smile, and she tugged her hair behind her ear. "I'll come find you after the meeting," she said. It wasn't a question.

"Okay," Tony agreed. His eyes followed her out of the room; the emergency lights were on in the hallways outside, but the workshop itself was still dark, lit only by the armors.

_"Sir, the power has now been completely restored,"_ J.A.R.V.I.S. informed him through Mark 43's speakers a moment later.

"Turn everything back on. Get Mark 44 back on the operating table."

_"Very well, sir,"_ J.A.R.V.I.S. responded and complied.

"You two: come over and help," Tony told the bots as Mark 44 returned to the table and settled down on it, powering down.

Dummy and You followed on his heels and started by stacking all the fallen, scattered tools back in their places.

It was a return to normalcy, more or less, but Tony knew it was too easily rattled by just a little shaking…

**The End**


End file.
